Refactor of the run scripts

[Whyborn]

The run scripts are currently quite monolithic and prescriptive. We want to separate the main working script, run_cable.sh into individual run scripts for each stage, i.e. run_climate_restart.sh, run_zero_biomass.sh etc. and separate the results into separate directories for each stage.

This allows is to retain information about the configuration of each stage. As it stands, the configuration options in the namelists are overwritten after each stage so there is no hard record of the configuration options used for each stage.

It should make it much easier to adapt scripts for the specific user's purpose, and make it easier for new users to understand the work flow.

There is likely to be a few iterations as we talk to users in the in Land Working group to get feedback.